Jeffrey Eugenides has spent nine years writing Middlesex, a comic epic concerning the transmission of a gene from a village in Asia Minor through twentieth-century Detroit to contemporary Berlin. Nine years is a lot of time for someone who had only published one previous, much slimmer novel, even taking into account the success of The Virgin Suicides. But worth it: Middlesex, which is much bigger in every sense, has just appeared in America to breathtakingly good reviews.

I met Jeffrey Eugenides in Café Einstein in Berlin, the city in which he has lived for the past three years with his wife, an artist, and their four-year-old daughter. (He was awarded a grant to write in Berlin for a year and they haven't yet got round to leaving.) The café makes a fleeting appearance in Middlesex, whose hero, like Eugenides, is a Greek-American raised in Detroit and now living in Berlin. So it seems appropriate to begin by asking how much of the novel is autobiographical.

'The story I am telling is very far from my own experience, so the only way I felt I could make it credible for me was to borrow from a certain amount of history and personal fact. It's autobiographical at the level of family detail or almost insignificant fact. I didn't set out to write about the Greek-American experience or originally to write a family saga at all. The idea was to write a fictional book about a hermaphrodite, and I wanted it to be medically accurate - to be a story of a real hermaphrodite, rather than a fanciful creature like Tiresias or Orlando who could shift in a paragraph; to avail myself of the mythological connections without making the character a myth.'

Middlesex is the story of Calliope Helen Stephanides, born with a mutation on her fifth chromosome which makes her appear at birth to be a girl, although she is, in fact, biologically and hormonally a boy. A charming, untroubled child, Callie is plunged into psychological and emotional chaos at adolescence when she starts sprouting facial hair, speaking in a deep voice, and falling in love with a girl in her Latin class.

5-alpha-reductase deficiency, the particular mutation that afflicts Callie, invariably occurs in inbred communities. 'That started me thinking about my Greek heritage and the village my grandparents came from and I realised I could tell a much larger story, the transmission of the gene, told by the final carrier of the gene,' says Eugenides.

In the process, he confronts the possibility that genetic determinism has revived ancient beliefs in destiny, disrupting our post-Freudian assumptions that character is overwhelmingly a product of experience. Fate may be down to evolutionary biology now, rather than the gods, but it is still in a fight to the death with free will.

The triumph of the novel - and the reason it took so long to write - is its voice. Calliope was the muse of epic poetry and, in the first half of the book, Eugenides's Callie recounts the odyssey of her grandparents' emigration from what is now Turkey to America. Desdemona and Lefty Stephanides flee the Turks attacking their Greek village only to find themselves caught up in the sacking of Smyrna. They make their way to Detroit, where they have a cousin, the only person left in the world who knows that they are not only husband and wife and third cousins, but also brother and sister.

'The first few years, I had a lot of difficulty with the voice. I had to get into the grandparents' heads, and it was a while before I gave myself permission to allow Callie that licence, to give her perhaps a little extra omniscience or allow her to create the story for the reader. The voice had to be capable of telling epic events in the third person and psychosexual events in the first person. It had to render the experience of a teenage girl and an adult man, or an adult male-identified hermaphrodite.'

As this suggests, Middlesex is, in a sense, two books in one, just as Callie is two sexes in one. The book is both family saga and coming-of-age novel, told from the outside and the inside. 'Since I was writing about the transmission of a genetic mutation, it seemed to me sensible and also incumbent on me to reiterate the transition in terms of the literary form. I hope the book quietly and not fist-poundingly moves from a more epic narration towards a more psychological novel.'

Dramatic public events - the burning of Smyrna, the race riots that drive the Stephanides family from downtown Detroit to the suburbs - are framed by the 41-year-old Cal, now an employee of the State Department. He flips backwards and forwards between omniscient storytelling and knowing, compromised interjection, in a triumph of structure and of engaging, wry wit.

Some aspects of the social history of Detroit (and so America) that are played out through the novel's rich texture are less successful than others. Fully two members of the Stephanides family get caught up in the beginnings of the Nation of Islam, in a section that stretched my credulity; and I didn't get the joke on Callie's brother's name, Chapter 11. I still didn't really get it when Eugenides explained that he goes bankrupt at the end (ie files for Chapter 11 bankruptcy in the US). And on the subject of names, both Eugenides and Callie grew up on Middlesex Boulevard, and the title is also, of course, a fine description of her predicament, so it is slightly unfortunate that, in Britain, the book sounds as if it is about a part of Greater London.

In The Virgin Suicides and again, in Middlesex, Eugenides says he has tried 'not to make something mundane strange, but rather, something that is somewhat freaky more normal'. Plotlines that concern five sisters who kill themselves or hermaphrodites may sound bizarre, but they are the stuff of our earliest and most potent stories. 'Latin literature, Ovid and Virgil, was the first writing I studied line by line. These were epics, sometimes epics of transformation, and when I look at my work I realise that influenced me enormously. Going down into the underworld, transformations: it seems to me that was what I was taught to think literature was. And when you think about what fiction can do that non-fiction can't: it is chart out the territory beyond realism to a certain extent.'

There is a nice postscript to the writing of Middlesex. Callie calls the girl with whom she falls in love the Obscure Object, after Buñuel. Both the Obscure Object's character and the events surrounding her are entirely invented, Eugenides says, but the term is from life. When he was an undergraduate at Brown University he and Rick Moody found the same girl attractive, and would say to each other, for example: 'Oh, I saw the Obscure Object today.' On the day he finished the manuscript of Middlesex, he says, he went to have dinner at the American Academy in Berlin. There was a woman there he vaguely recognised. Sure enough, she was the Obscure Object. Makes you wonder about fate.

· Jeffrey Eugenides will be in conversation with Mariella Frostrup on Wednesday 9 October at the Apollo Theatre, Shaftesbury Avenue, London WC2 (0207 494 5540)